Group 18: Differencial expression of genes in cancer

Introduction 1

{output: false} According to the instructions of leon, we need a 10 slide presentations so we could have the following structure:

Introduction

Data and problem to analyze
visuzalization of data

Materials and Methods

Libraries needed and why we are using them (recount and )
Which analsysis we did to the data

Results

Graphs with most important results

Disucssion

Biological insights of results
Conclusion based on insights

Introduction:

Many subtypes require a large collection of data

Question: Which genes are differentially expressed in different subtypes of cancer

Materials and Methods 1

General wokflow

Materials and Methods 2:

Considerations about the data:
- Excluded men as they represented a very small portion of the study
- We removed uninteresting genes (variance across samples of 0)
- Removed NAs and merged metadata with counts data

Male-female ratio

DESEQ Analysis:

Male-female ratio

We can see that many of the differentially expressed genes are on the left side of the volcano plot.

DESEQ Analysis: Top pathaways affected by DE genes

PCA Analysis:

Here is an analysis of PCA plots showing the scree and cumulative variance explained.

The high dimentionality required to explain 85% of the variablity of the data shows that cancer is a difficult task

PCA Analysis:

Overlapped clustering of patients

The clusters from patients with and without tumor overlap, meaning the PCA is not separating clearly the clusters.

Discussion: Biological insights

We can see that the DE genes in the data affect most importantly X pathways
THis makes/not makes sense with the literature as 1,2,3

Conclusion:

Next steps:

Clustering of DE genes
Identification of more subtypes with clustering